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Open Notebook Science


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An invited talk at the Austrian Science Fund (FWF) highlighting the importance of Open Notebook Science and Jean-Claude Bradley.

Published in: Science, Technology
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Open Notebook Science

  1. 1. Open Notebook Science Peter Murray-Rust* and Michelle Brook, Open Knowledge and University of Cambridge FWF, Vienna, AT, 2014-06-03 *Shuttleworth Fellow 2014-5
  2. 2. Overview • Most scientific data is lost; costs many billions… • … AND LIVES. Closed Data Means People Die • Human problem; lack of vision + active opposition. • Fully open data can change this • Appreciation of Jean-Claude Bradley’s work • Panton Fellows (Ross Mounce, Sophie Kershaw) • Content Mining - interim solution (Hargreaves UK) • Digital Enlightenment or Digital Darkness? • WHAT CITIZENS CAN and MUST DO
  3. 3. [at Research Data Alliance, we are entering a new “era of open science”, which will be “good for citizens, good for scientists and good for society”. She explicitly highlighted the transformative potential of open access, open data, open software and open educational resources – mentioning the EU’s policy requiring open access to all publications and data resulting from EU funded research. kroes/#sthash.3SWDXDE6.dpuf RCUK Wellcome ERC NSF FWF… require fully OPEN
  4. 4. PMR’s Tribute Planned Memorial Meeting July 14th 2014 Cambridge OPEN NOTEBOOK SCIENCE
  5. 5. Award of Blue Obelisk Jean-Claude Bradley Egon Willighagen
  6. 6. Traditional Research and Publication “Lab” work paper/th esis Write rewrite Re-experiment publish ??? Validation?? DATA output “belongs” to publisher
  7. 7. Elsevier wants to control Open Data [asked by Michelle Brook]
  8. 8. MLB – 300 seconds
  9. 9. Free/Open Software Development Engineered repository World community CODE rewrite validate CODE fork CODE Re-use CODE Re-use Github, BitBucket StackOverflow, Apache inspires OSI Example: ContentMine at
  10. 10. Open Source software inspires Open Science Jean-Claude Bradley 2006
  11. 11. Open Notebook Science, ONS Jean-Claude Bradley 2006
  12. 12. Jean-Claude Bradley 2006
  13. 13. Jean-Claude Bradley 2006
  14. 14. Jean-Claude Bradley 2006
  15. 15. And spectra were included as well Jean-Claude Bradley 2006
  16. 16. TOOLS Open Notebook Science Open engineered repository World community INSTRUMENT validate merge MODEL CODE DATA DATA knowledge calibrate Problems are solved communally; Nothing is needlessly duplicated; “publication“ is continuous ; data are SEMANTIC Machines and humans Working together
  17. 17. Mat Todd, University of Sydney: Antimalarial
  18. 18. Medicinal Chemistry: Make thousands of similar compounds till you get one suitable; O Instead of N is 300 times better
  19. 19. The economic value of data • I believe that we spend globally ca 400 billion USD / yr on public research. • The outputs include: – Knowledge / papers / patents – Organizations – People – Materials – Data – many billions/year and much is lost
  20. 20. US Taxpayers spend 139 Billion USD / yr on Scientific Research 4 Billion USD on human genome yielded 800 Billion USD and 4 M job-years
  21. 21. …three problems—flawed design, non- publication, and poor reporting—together meant >85% of research funds were wasted, a global total loss >100 billion USD per year. [Lancet 2009] [Even more] waste clearly occurs after publication: from poor access, poor dissemination, and poor uptake of the findings of research. [PLOS Medicine 2014-05-27] Bad publication wastes science
  22. 22. Citizens pay $400,000,000,000 Value : ??? … cost $300,000 each to create … for research in 1,500,000 articles $7000 each to “publish” costs $10,000,000,000 “publishers” forbid access to 99.9% of citizens of the world
  23. 23. Where is the Digital Enlightenment? • Science is done in C20th ways … • …communicated in C19th ways … • … losing the power of C21st
  24. 24. discovery/
  25. 25. The Polymath project Tim Gowers and the world
  26. 26. “Free” and “Open” • "Free software is a matter of liberty, not price. ’free speech', not 'free beer'”. (R M Stallman) • “A piece of data or content is open if anyone is free to use, reuse, and redistribute it” (OKFN) • “open” (access) has multiple incompatible “definitions”. Major split is “human eyeballs” vs copying and machine “reusability” • “Open” is a marketing term for publishers, who frequently (often deliberately) do not grant full Openness. “Gratis” vs “Libre”
  27. 27. 4 Freedoms (Richard Stallman) • Freedom 0: The freedom to run the program for any purpose. • Freedom 1: The freedom to study how the program works, and change it to make it do what you wish. • Freedom 2: The freedom to redistribute copies so you can help your neighbor. • Freedom 3: The freedom to improve the program, and release your improvements (and modified versions in general) to the public, so that the whole community benefits. "I’ve spent a third of my life building software based on Stallman’sfour freedoms, and I’ve been astonished by the results. WordPress wouldn’t be here if it weren’t for those freedoms, and it couldn’t have evolved the way it has.” - Matt Mullenweg, co-creator of WordPress
  28. 28. Critical Historical Open Events • Free Software Foundation (RMS, 1985) and Linux (Torvalds, 1991) • The World Wide Web (TBL, 1991) • The human genome (1990-2001) The life of Aaron Swarz (1986-2013)
  29. 29. • Automatic release of sequence assemblies larger than 1 kb (preferably within 24 hours). • Immediate publication of finished annotated sequences. • Aim to make the entire sequence freely available in the public domain for both research and development in order to maximise benefits to society.
  30. 30. … an unprecedented public good. … … completely free and unrestricted access to [peer- reviewed literature] by all scientists, scholars, teachers, students, and other curious minds. … …Removing access barriers to this literature will accelerate research, enrich education, share the learning of the rich with the poor and the poor with the rich, make this literature as useful as it can be, and lay the foundation for uniting humanity in a common intellectual conversation and quest for knowledge. (Budapest Open Access Initiative, 2003)
  31. 31. Authors don’t deposit data (Ross Mounce)
  32. 32. Restrictions on Re-use of Crystallographic data NOTE: The CCDC is based on data contributed by scientists as part of publication and validation
  33. 33. Mendeley From Wikipedia, the free encyclopedia • … a social media site used by many scientists to store metadata … • … purchased by Elsevier in 2013 • David Dobbs, in The New Yorker, described motive as: – to acquire its user data, – to destroy or coöpt an open-science icon that threatens its business model. • PM-R: Mendeley can also Snoop and Control
  34. 34. Panton Principles for Open Data in science(2010) • PUBLISH YOUR DATA OPENLY • …make an explicit and robust statement of your wishes. • Use a recognized waiver or license that is appropriate for data. • open as defined by the Open Knowledge/Data Definition (… NOT non-commercial) • Explicit dedication of data … into the public domain via PDDL or CCZero Peter Murray-Rust, Cameron Neylon, Rufus Pollock, John Wilbanks
  35. 35. Panton Authors and Fellows
  36. 36. Sophie Kershaw, Panton Fellow : Doctoral Training in Oxford
  37. 37. “Train a new generation of data scientists and broaden public understanding” “Riding The Wave” European Commission October 2010
  38. 38. Sophie Kershaw, Panton Fellow
  39. 39. Rotation-Based Learning (RBL) Phase 1: Initiator • No communication permitted between groups • Attempt to reproduce existing literature • Deliver a coherent research story by the end of Phase 1 Phase 2: Successor • Communication between groups still prohibited • Validate and develop the inherited research story • Critique your predecessors • Role of research producer vs. research user • Can this approach help to foster awareness of reproducibility issues? Throughout Phases 1 & 2: • Daily lectures on open science culture & techniques • First-hand application to own research work • Version control using GitHub • Daily group supervision
  40. 40. “Do you think you would be more confident in the future about trying to apply Open techniques to your work..?” • 50% Yes, by myself • 41% Yes, with help/guidance • 9% No opinion/neutral • 0% No
  41. 41. Ross Mounce (Bath), Panton Fellow • Sharing research data: • How-to figures from PLOS/One [link]: Ross shows how to bring figures to life: • PLOSOne at • PLOS at (demo)
  42. 42. TOOLS Open Notebook Science Open engineered repository World community INSTRUMENT validate merge MODEL CODE DATA DATA knowledge calibrate Problems are solved communally; Nothing is needlessly duplicated; “publication“ is continuous Machines and humans Working together CC-BY
  43. 43. Traditional Research and Publication “Lab” work paper/th esis Write rewrite Re-experiment publish ??? Validation?? DATA output “belongs” to publisher Is there anything we can do with this?
  44. 44. Content Mining (TDM) “Lab” work paper/th esis Write publish ??? DATA Intelligent software to read scientific papers DATA Publishers have tried to stop us mining it. On 2014-06-01 IT BECAME LEGAL IN UK! The Right To Read Is The Right To Mine
  45. 45. Content Mining • 1,000,000 papers/year => 3,000 / day => 2 /min • 10,000+ phylogenetic trees (Ross Mounce, BBSRC) • 20,000 chemical reactions / day • >> 1 million graphs, plots, bar charts, statistics • Possible on a laptop •
  46. 46. AMI2: High-throughput extraction of semantic chemistry from the scientific literature Andy Howlett, Mark Williamson, Peter Murray-Rust, Unilever Centre, Cambridge
  47. 47. AMI2 is a framework that can extract semantic data from the scientific literature.
  48. 48. AMI2 architecture
  49. 49. Visitor Design Pattern/Example Visitor= something that extracts a specific type of data SpeciesVisitor, ChemVisitor, PhylogeneticTreeVisitor, GeoLocationVisitor, ClinicalTrialVisitor … Visitable= something that can have specific data extracted PDF, SVG, Table
  50. 50. ChemistryVisitor Can interpret diagram or look up chemistry in PubChem or ChEBI
  51. 51. PhylogeneticTreeVisitor
  52. 52. 1) SpeciesVisitor
  53. 53. 2) ChemistryVisitor
  54. 54. 3) PhylogeneticTreeVisitor
  55. 55. C) What’s the problem with this spectrum? Org. Lett., 2011, 13 (15), pp 4084–4087 Original thanks to ChemBark
  56. 56. After AMI2 processing….. … AMI2 has detected a square
  57. 57. TOOLS Open Notebook Science Open engineered repository World community INSTRUMENT validate merge MODEL CODE DATA DATA knowledge calibrate Problems are solved communally; Nothing is needlessly duplicated; “publication“ is continuous Machines and humans Working together CC-BY
  58. 58. Thanks • BBSRC for PLUTo project (Bath) • Unilever Research for PhD (Andy Howlett) • TechnologyStrategyBoard / CambridgeIP (PDRA Mark Williamson) • Shuttleworth Foundation (Fellowship PM-R) • Julian Huppert MP and David Willetts (support for Hargreaves copyright reform) • Christoph Steinbeck (EBI) Metabolights • The ContentMine team (Michelle Brook, Ross Mounce, Jenny Molloy, Richard Smith-Unna, CottageLabs) • The Blue Obelisk • Open Knowledge • Apache PDFBox and all F/LOSS software authors • Unilever Centre and University of Cambridge
  59. 59. CLOSED ACCESS MEANS PEOPLE DIE • Create Open Notebook Science in your discipline • Actively release data into Public Domain. • Actively campaign against any re-use restrictions (including CC-BY-NC) • Refuse to work with closed organizations • Convince Academia to Open its doors CLOSED DATA MEANS PEOPLE DIE
  60. 60. there-yet economics-of-academic-publishing/ _Genome/publicat/BattelleReport2011.pdf NG9A&feature=youtube_gdata mins 5-9 Some references